Plot hole: There are six metal bars mounted around the circumference of the water wheel's axle. In the wheel's interior, when Jack frees himself he lands on his feet, begins to run and promptly hits his head on one of those axle bars, then falls out. Moments later, when Jack returns and runs in the wheel, he is shorter (way more than a foot) than all six spinning axle bars, which would make that previous shot impossible, however humorous it is. (01:52:40 - 01:53:55)Super Grover
Plot hole: The snakes are contained in the cargo hold which is shown to be unpressurised on this aircraft (there is an altimeter which releases the snakes after it hits 35000 feet - if the hold was pressurised it would level off at cabin pressure, which is about 8,000 feet). A cargo door is left open to allow the snakes into the passenger compartment, but this would either cause the plane to not pressurise properly, causing everyone on board severe breathing problems if not worse, or would keep the hold at cabin pressure, meaning the altimeter would never reach the right level to release the snakes.
Plot hole: When Magneto lands the bridge between San Francisco and Alcatraz, only the ends of the bridge are on land, with the rest still suspended in the air despite having nothing to keep it there. Magneto could arguably be using his powers to keep it supported, but at the moment he loses his powers it still does not collapse at the center.
Plot hole: When we see the Zenith Team playing softball, it's a scene taken from later in the movie. For one thing, Mr. Pibb is there, even though we don't meet him until the next scene. Second, they're in the room with the UFO, but we don't see that until later. Finally, Zoom's outfit is different than the last scene, but in the next scene he's wearing the same outfit.Brad
Plot hole: Alex and Jack go to Liverpool St. Station to find the guys from Jeff Slater's. This is on the day of the funeral, otherwise it would make no sense going there. But when Mrs Jones sees Alex, she says "shouldn't you be at school?" This makes no sense because Alex would not go to school on the day of the funeral. It's not a character mistake because Mrs. Jones would never make that mistake.
Plot hole: When Oleg calls Teresa from the pedophile's playroom, he tells her the address of their house: 1456 Owens Park Lane, Hoboken. When Teresa shows up, she tells the pedophile that he called from this apartment, 1456 Owens Park Lane, Apartment 303. Oleg never told her what apartment number he was in.
Plot hole: Right at the end when Pete calls for the "Hard Car" to evacuate the president, he gives very specific orders as to the evacuation point. Considering he was to be arrested on sight, there is no way he would know any of the security arrangements and they would surely have changed them radically because he was such a senior agent. The Secret Service is constantly changing their security.
Plot hole: When 02 is carjacked, he runs after his vehicle for some distance. When he finally gives up, he looks into a nearby alley and sees Coco, the girl who initially marked him for the carjacking. This conveniently moves the story along, but makes no sense. She could not have run that distance so quickly, nor would she have reason to follow him.
Plot hole: Just before the bomb explodes at the beginning of the movie, the guard is looking for the car playing 'don't worry baby' on it's stereo. In the final timeline the disaster has been averted, the bomb having gone off, and the ferry docked. After this, when Carlin is in the car, the same song is playing, but the bomb was set to a timer.